Hi Chris, I think you are a little stuck. One thing you can do is to run recon-all with the -no-ba-labels switch as the last arg. This will prevent it from running that part of the code. You might then be able to run recon-all with only the -ba-labels switch in a separate process.

doug

Chris wrote:

I have a tricky situation where we can't use symbolic links ( cifs/smb mounts ) and it doesn't make sense to copy the fsaverage to the SUBJECTS_DIR. The subjects_dir is actually a separate directory for every subject when trying to run things through the connectome toolkit.

I've edited my own version of recon-all in attempts of passing full paths to some of the tools if necessary. I'm getting caught in the mri_label2label step, since its using "--srcsubject" and "--srclabel"

Passing a full path to "--srcsubject" doesn't work as expected, since its assuming the path of --srcsubject exists inside my SUBJECTS_DIR. If i only pass the default "fsaverage", then that also doesn't work because it doesn't exist inside my SUBJECTS_DIR either.

Any suggestions? -Chris

[petty@node61 free]$ mri_label2label --srcsubject /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage --srclabel /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/label/lh.BA1.label --trgsubject test20090520_36099 --trglabel ./lh.BA1.label --hemi lh --regmethod surface

srclabel = /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/label/lh.BA1.label srcsubject = /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage trgsubject = test20090520_36099 trglabel = ./lh.BA1.label regmethod = surface

srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0

SUBJECTS_DIR /mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free/ FREESURFER_HOME /usr/local/packages/freesurfer_v5.1.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free///usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/surf/lh.sphere.reg

MRISread(/mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free///usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/surf/lh.sphere.reg): could not open file No such file or directory ERROR: could not read /mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free///usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/surf/lh.sphere.reg

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